Work described herein was funded by the Howard Hughes Medical Institute.
The surface glycoproteins of enveloped viruses play critical roles in the initial events of viral infection, mediating virion attachment to cells and fusion of the viral and immune response in infected hosts. Envelope glycoproteins are also major targets for the anti-viral immune response in infected hosts. The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein consists of two noncovalently associated subunits, gp120 and gp41, that are generated by proteolytic cleavage of a precursor polypeptide, gp160. Luciw, P. A., In Fields Virology, Third Edition, B. N. Fields et al., eds., Lippincott-Raven Publishers, Philadelphia, pp. 1881-1952 (1996); Freed, E. O. et al., J. Biol. Chem. 270: 23883-23886 (1995). gp120 directs target-cell recognition and viral tropism through interaction with the cell-surface receptor CD4 and one of several co-receptors that are members of the chemokine receptor family. Broder, C. C. et al., Pathobiology 64:171-179 (1996); D""Souza, M. P. et al., Nature Med. 2:1293-1300 (1996); Wilkinson, D., Current Biology 6:1051-1053 (1996). The membrane-spanning gp41 subunit then promotes fusion of the viral and cellular membranes, a process that results in the release of viral contents into the host cell. It has not yet been possible to obtain a detailed structure for gp41, either alone or in complex with gp120.
Described herein is the crystal structure of the xcex1-helical domain of the gp41 component of HIV-1 envelope glycoprotein which represents the core of fusion-active gp41. Also described herein is Applicants"" determination, with reference to the crystal structure, that certain amino acid residues within the core are essential for interaction of the component peptides and, thus, for gp41 activity. The core of fusion-active gp41 is composed of a trimer of two interacting peptides, referred to here as N36 and C34. The minimal stable envelope subdomain has been shown to consist of a 36-residue peptide (N-36) and a 34-residue peptide (C-34) whose amino acid sequences are presented below. The crystal structure of the N36/C34 complex is a six-helix bundle in which three N36 helices form an interior, parallel coiled coil and three C34 helices pack in an oblique, anti-parallel manner into highly conserved, hydrophobic grooves on the surface of the N36 trimer. It shows striking similarity to the low-pH induced conformation of influenza hemagglutinin (HA).
Applicants have determined the structural basis for interaction between two peptide fragments of HIV gp41: one peptide fragment derived from the N-terminal region of the ectodomain of gp41 and one peptide fragment derived from the C-terminal region of the gp41 ectodomain. The N-terminal peptide fragment, N36, includes amino acid residue 546 through and including amino acid residue 581, numbered according to their position in HIV-1 gp160; it includes amino acid residues which comprise a region of the ectodomain which encompasses the 4-3 hydrophobic repeat. The amino acid sequence of the N36 peptide is:
SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL (SEQ ID NO.: 1).
The C-terminal region peptide fragment C34 includes amino acid residue 628 through and including amino acid residue 661, numbered according to their position in HIV-1 gp160; it is derived from the region prior to the transmembrane segment. The amino acid sequence of the C34 peptide is:
WMEWDREINNYTSLIHSLIEESQNQQEKNEQELL (SEQ ID NO.: 2). The three-dimension coordinates for the atoms in the N36/C34 gp41 complex are presented herein. They can be used to display the structure of the complex and to design molecules (drugs) which interact with gp41 and inhibit its activity, such as those which prevent interaction of key components (amino acid residues) of the xcex1-helical domain which represents the core of fusion-active gp41.
Work described herein provides, for the first time, an understanding of how the N-terminal peptide and the C-terminal peptide interact. The crystal structure and information regarding the interactions of these two peptides provide the basis for development of drugs which inhibit HIV infection, such as peptidomimetic or small-molecule inhibitors, using such methods as combinatorial chemistry or rational drug design. Drugs developed or identified with reference to the information provided herein are also the subject of the present invention. Drugs which fit into or line the N-peptide cavity, prevent the N-peptide cavity from accommodating amino acid residues or peptides from the C-terminal region of gp41 and, thus, prevent or inhibit gp41 activity are the subject of this invention. Such drugs can be identified with reference to the information about the structure of the complex and the cavity shown to be present in the N36 trimer, provided herein, or with reference to information about the structure of the complex and the three dimensional coordinates of the cavity, also provided herein, and known methods. In a particular embodiment of identifying or designing a molecule which inhibits the fusion active form of gp41 and, thus, inhibit HIV, in which combinatorial chemistry is used, a library biased to include an increased number of indole rings, hydrophobic moieties and/or negatively charged molecules is used. An antibody which binds these key areas of fusion-active gp41 is also the subject of the invention. For example, an immunogen which is or includes a molecule with the coordinates described herein or the N-peptide core can be used to immunize an individual, resulting in production of antibodies that bind the cavity or pocket on the N-terminal peptide and, thus, render it unavailable for its normal interactions and prevent or inhibit gp41 activity.